The analysis of temporal patterns in water quality and benthic assemblages in estuaries constitutes an important methodological issue for discriminating the effects of natural and anthropogenic pressures.
Temporal trends in water quality and in the subtidal benthic community over a 5-year interval in the Mondego estuary (Portugal) were investigated with the aim of assessing changes in environmental quality as a response to restoration efforts and climate variability. Particularly, we addressed the following questions: (a) Would trends in water quality and benthos behave consistently over the whole study period for the different zones of the monitoring network and indicate improvement or degradation in ecological condition? (b) Could we distinguish the effects of climate variability and restoration efforts in
water quality and benthos from trend analysis results? (c) Could the response of the benthic communities and water quality be useful to guide the planning of future management actions in this system?
Clear cause–effect relationships regarding the ecological response to restoration efforts and climate variability were indeed challenging to identify and interpret. In fact, the response of water quality and
benthic communities to restoration efforts seemed to have been masked by the effects of climatic variability.
Furthermore, the present study illustrated clearly the high environmental variability inherent to estuarine systems and the difficulty of clearly distinguishing natural from anthropogenic stressors, in agreement with the “Estuarine Quality Paradox”. Implications for ecological quality assessment and management of the Mondego estuary and other poikilohaline systems are discussed, namely with regard to the “one-out, all-out” principle required by the European Water Framework Directive (WFD).